Stoch produced a fine second jump of 130m, after a first of 132m, to overhaul Gregor Schlierenzauer and who he had overtaken in the World Cup standings on Saturday.
The Polish ski jumper finished second in the first of two events in Engelberg while the defending World Cup and Four Hills champion was well down in 27th to relinquish his lead.
Stoch took the second victory and his second of the season with a total of 274.7 points with Andreas Wellinger second with 270.8 and Saturday's winner and Polish teammate Jan Ziobro third.
He now leads Schlierenzauer in the overall World Cup rankings by 58 points but, with the Four Hills set to start on December 28, he wants to enjoy the days in between first.
"It has been a good weekend for the Polish team with Jan's win and now mine. I am proud of us," said Stoch.
"It was a great moment for me on Saturday, it was one of my dreams to get the yellow jersey heading into the Four Hills. It is a nice Christmas present for me.
"Maybe I am now the favourite but I am not focussing on that. I want to rest and do my best and then see what happens."
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